Comoviruses are a group of plant viruses in the picornavirus superfamily. The type member of comoviruses, cowpea mosaic virus (CPMV), was crystallized in the cubic space group I23, a = 317 A and the hexagonal space group P6(1)22, a = 451 A, c = 1038 A. Structures of three closely similar nucleoprotein particles were determined in the cubic form. The roughly 300-A capsid was similar to the picornavirus capsid displaying a pseudo T = 3 (P = 3) surface lattice. The three beta-sandwich domains adopt two orientations, one with the long axis radial and the other two with the long axes tangential in reference to the capsid sphere. T = 3 viruses display one or the other of these two orientations. The CPMV capsid was permeable to cesium ions, leading to a disturbance of the beta-annulus inside a channel-like structure, suggesting an ion channel. The hexagonal crystal form diffracted X rays to 3 A resolution, despite the large unit cell. The large ( approximately 200 A) solvent channels in the lattice allow exchange of CPMV cognate Fab fragments. As an initial step in the structure determination of the CPMV/Fab complex, the P6(1)22 crystal structure was solved by molecular replacement with the CPMV model determined in the cubic cell.

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Glutamate dehydrogenase (GDH) is found in all organisms and catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate. Unlike GDH from bacteria, mammalian GDH exhibits negative cooperativity with respect to coenzyme, activation by ADP, and inhibition by GTP. Presented here are the structures of apo bovine GDH, bovine GDH complexed with ADP, and the R463A mutant form of human GDH (huGDH) that is insensitive to ADP activation. In the absence of active site ligands, the catalytic cleft is in the open conformation, and the hexamers form long polymers in the crystal cell with more interactions than found in the abortive complex crystals. This is consistent with the fact that ADP promotes aggregation in solution. ADP is shown to bind to the second, inhibitory, NADH site yet causes activation. The beta-phosphates of the bound ADP interact with R459 (R463 in huGDH) on the pivot helix. The structure of the ADP-resistant, R463A mutant of human GDH is identical to native GDH with the exception of the truncated side chain on the pivot helix. Together, these results strongly suggest that ADP activates by facilitating the opening of the catalytic cleft. From alignment of GDH from various sources, it is likely that the antenna evolved in the protista prior to the formation of purine regulatory sites. This suggests that there was some selective advantage of the antenna itself and that animals evolved new functions for GDH through the addition of allosteric regulation.

The three-dimensional structure of intact human rhinovirus 14 (HRV-14) complexed with Fab fragments (Fab17-IA) from a strongly neutralizing antibody that binds bivalently to the virion 1,2 has been determined to 4.0 Å resolution by a combination of X-ray crystallography and cryoelectron microscopy. In contradiction to the most commonly held model of antibody-mediated neutralization, Fab17-IA does not induce a conformational change in the HRV-14 capsid. Instead, the paratope of the antibody undergoes a large conformational change to accommodate the epitope. Unlike any previously described antibody-antigen structure, the conserved framework region of the antibody makes extensive contact with the viral surface. Fab17-IA penetrates deep within the canyon in which the cellular receptor for HRV-14 binds 3,4 . Hence, it is unlikely that viral quaternary structure evolves merely to evade immune recognition. Instead, the shape and position of the receptor-binding region on a virus probably dictates receptor binding and subsequent uncoating events and has little or no influence on concealing the virus from the immune system.The capsid of HRV-14 is composed of 60 copies of four viral proteins, VP1-VP4. Each of the first three proteins has a relative molecular mass of ~30,000 (M r ~ 30K) and a similar ²-barrel structure. The smaller VP4 (M r ~ 7K) lies at the capsid-RNA interface with an extended structure 3 . The monoclonal antibody 17-IA binds to the NIm-IA site which was defined by natural escape mutations at residues D1091 and E1095 on the B-C loop of VP1 (the first digit designates the viral protein and the remaining three designate the residue number). The NIm-IA epitope lies at the 'north rim' of a depression (canyon) on the viral surface that encircles each of the five-fold icosahedral axes of the virus 3 and is where the receptor, ICAM-1, binds 4 . The variable domains (V H · V L ) of Fab17-IA make extensive contact with both the north and south walls of the canyon region. At the north wall, the antigen-binding region (paratope) contacts ~550 Å 2 of the viral surface around NIm-IA site (Fig. 1). The heavychain hypervariable region dominates the contact surface: 23 residues from the heavy chain but only 9 residues from the light chain. As was proposed on the basis of cryo-electron microscopy on this HRV/Fab complex 5 , coulombic interactions dominate the paratopeepitope interface with roughly two-thirds of the total buried viral surface being contributed CORRESPONDENCE and requests for materials should be addressed to H.R.B. (hbourne@quickmail.ucsf.edu). Although somatic mutations occur throughout the variable domain 7 , it is unlikely that mutations in these framework sites that contact the viral surface are merely coincidental. NIH Public AccessSeveral large changes in the Fab17-IA structure accompany binding to HRV-14, although the virus capsid remains essentially rigid (Fig. 2a). A large conformational change occurs in the heavy-chain CDR3 loop (Fig. 2b, c, d) where the Cα atom of Tyr102 H moves up to 5...

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Nearly 20 percent of the packaged RNA in bean-pod mottle virus (BPMV) binds to the capsid interior in a symmetric fashion and is clearly visible in the electron density map. The RNA displaying icosahedral symmetry is single-stranded with well-defined polarity and stereochemical properties. Interactions with protein are dominated by nonbonding forces with few specific contacts. The tertiary and quaternary structures of the BPMV capsid proteins are similar to those observed in animal picornaviruses, supporting the close relation between plant comoviruses and animal picornaviruses established by previous biological studies.

The structure of cucumber mosaic virus (CMV; strain Fny) has been determined to a 3.2-Å resolution using X-ray crystallography. Despite the fact that CMV has only 19% capsid protein sequence identity (34% similarity) to cowpea chlorotic mottle virus (CCMV), the core structures of these two members of the Bromoviridae family are highly homologous. As suggested by a previous low-resolution structural study, the 305-Å diameter (maximum) of CMV is ϳ12 Å larger than that of CCMV. In CCMV, the structures of the A, B, and C subunits are nearly identical except in their N termini. In contrast, the structures of two loops in subunit A of CMV differ from those in B and C. These loops are 6 and 7 residues longer than the analogous regions in CCMV. Unlike that of CCMV, the capsid of CMV does not undergo swelling at pH 7.0 and is stable at pH 9.0. This may be partly due to the fact that the N termini of the B and C subunits form a unique bundle of six amphipathic helices oriented down into the virion core at the threefold axes. In addition, while CCMV has a cluster of aspartic acid residues at the quasi-threefold axis that are proposed to bind metal in a pH-dependent manner, this cluster is replaced by complementing acids and bases in CMV. Finally, this structure clearly demonstrates that the residues important for aphid transmission lie at the outermost portion of the ␤H-␤I loop and yields details of the portions of the virus that are hypothesized to mediate binding to aphid mouthparts.Cucumber mosaic virus (CMV) is the type member of the genus Cucumovirus, family Bromoviridae, which infects over 800 plant species and causes economically important diseases of many crops worldwide (18). CMV isolates are divided into two main subgroups based on their serological and nucleic acids properties (18). Serologically, the two subgroups are closely related, as has been shown by cross-reactivity to polyclonal antibodies (18, 29). Some monoclonal antibodies produced against the coat proteins of subgroups I and II can differentiate the two, indicating the presence of unique epitopes for each (22,29).Recently, the molecular structure of CMV was determined to ϳ8-Å resolution using cryo-transmission electron microscopy (cryo-TEM) and X-ray crystallography (30). A remarkable similarity was demonstrated between the structure of CMV and that of cowpea chlorotic mottle virus (CCMV), another member of the Bromoviridae. In CCMV, the N termini of the B and C subunits form an unusual ␤-hexamer at the icosahedral threefold axes (27). This structure is believed to also exist in CMV (30) and is a variant of the ␤-annulus observed in many plant virus capsids. The domain connecting the N-terminal basic R domain to the ␤-barrel domain has been observed in the electron densities of the C subunits in several Tϭ3 plant viruses, including southern bean mosaic virus (1) and tomato busy stunt virus (6). The N-terminal arms of the three C subunits extend along an inner edge of the protein shell and loop around the threefold axes, interdigitating in sets of thr...